Anxieties about protection for Scotland's wildlife and countryside have deepened after it emerged that Scottish Natural Heritage, the conservation agency, is to lose more than £16m in funding over the next three years.

The agency's annual budget will fall from £60.7m last year down to £53m by 2014/15, a total cut in cash terms of £16.1m, without including inflation. In three years time, SNH will be left with cuts close to 85% of its current funding and, say conservationists, worrying impacts on its expertise as a result.

First raised in a Guardian story over Christmas, senior conservationists now fear the funding shortfall will damage SNH's ability to protect Scotland's environment, after the end of its five year "species action framework" at the end of March.

The reductions, imposed by John Swinney, the Scottish finance secretary, as focused public spending cuts on less politically damaging areas for the Scottish National party, have led to a further wave of job losses at the agency.

After cutting 42 posts last year, and ending a number of short-term and temporary contracts, SNH has just lost another 53 experienced staff through voluntary redundancy, saving about £3m in total. The agency's budget, at £60.7m last year, has been cut to £57.8m this year, £55.2m next year and £53m in 2014/15.

Ecologists and conservationists now fear that shedding nearly 100 staff will impact on the quality and effectiveness of its activities, although SNH says some projects will continue getting central Scottish government funding through its rural development spending.

SNH's partner agencies are now pressing it to confirm that it will continue its three-pronged approach on the environment: targeting protection of the most vulnerable species, protecting key habitats identified in the EU's Natura 2000 programme, while still going for massive, landscape level eco-system projects.

SNH said it had protected funding for several key, high profile and valuable projects profiled in our story in December: the Save Scotland's Red Squirrel project has its £175,000 a year funding secured, and SNH's schemes to eradicate invasive species such as American signal crayfish and rhodendron.

So too, said a spokesman, has the final year of the sea eagle reintroduction programme, the last year of the American mink eradication scheme in the Hebrides, and the beaver reintroduction project at Knapdale (a scheme rendered somewhat moot given there are probably 130 or so beavers now living wild on Tayside and beyond). He added:

The management of invasive non native species remains among our highest priorities, particularly in relation to crayfish and rhoddodendrun, so resources will continue to be targeted at this area of our work, possibly even increasing.

The agency is also drafting a new "wildlife management framework" which will target "conflict species" such as red deer and hen harriers, and reintroduced animals, as well as some of the 22 most vulnerable species on the species action framework.

But to protect these core programmes it had been forced to reject nine funding bids and has "reduced our commitment to a further 12 due to limited resources," a spokesman said. Most have had between £3,000 and £25,000 cut. For projects such as the Aberdeen Greenspace Project, that included cuts in their cash or in the length of a project.

One prominent project which was under threat is run by Butterfly Conservation Scotland, and protects several very rare, even unique, butterflies listed on the species action framework, including the pearl-bordered fritillary, the marsh fritillary and the slender Scotch burnet moth.

The BCS project has had a 25% cut in the budget it requested, but SNH has been able to find stop-gap funding from another pot of money to secure its longer-term survival. The BCS programme worked by getting farmers to apply for agri-environment funding; normally a pretty challenging task for individual farmers, it has had a 90% success rate.

Paul Kirkland, director of Butterfly Conservation Scotland, said they were delighted that SNH had salvaged the project for now but their "big worry" was the loss of some of the agency's most experienced staff. He said:

It's a great worry that they're losing very experienced naturalists, conservationists and ecologists. The new people that are coming on board are very enthusiastic and very bright, but it's the lack of long-term expertise which is very worrying. Some of those are our key contacts.